X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 3.5
Temperature 288.0
Details Sodium phosphate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 72.58 α = 90
b = 72.58 β = 90
c = 141.84 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IIC -- --
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 1.5418 -- --

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.29 30 84.3 0.092 -- -- -- 17925 15102 -- -- --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.286 2.3 62.1 0.211 -- -- -- --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.286 10.0 -- 0.0 17290 14759 1494 85.4 -- -- 0.197 0.239 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.3 2.38 1278 117 -- 0.2178 0.2486 -- 75.7
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 2.326
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.326
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.653
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.76
c_dihedral_angle_d 24.97
c_angle_deg 1.23
c_bond_d 0.006
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.24
Luzzati Sigma A (Observed) 0.2
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.3
Luzzati Sigma A (R-Free Set) 0.23
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1908
Nucleic Acid Atoms 0
Heterogen Atoms 22
Solvent Atoms 130

Software

Computing
Computing Package Purpose
R-AXIS Data Reduction (intensity integration)
R-AXIS Data Reduction (data scaling)
CNS Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
CNS model building
R-AXIS data reduction
R-AXIS data collection